Variant report

Variant	rs4995899
Chromosome Location	chr17:46150730-46150731
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:46147297..46149380-chr17:46149776..46151731,2	K562	blood:
2	chr17:46113009..46115141-chr17:46150190..46153046,2	MCF-7	breast:
3	chr17:46149832..46152241-chr17:46177929..46179581,3	MCF-7	breast:
4	chr17:46150171..46152503-chr17:46178704..46181546,2	K562	blood:
5	chr17:46143868..46147268-chr17:46149730..46155245,6	K562	blood:
6	chr17:46130466..46133390-chr17:46149390..46151552,2	MCF-7	breast:
7	chr17:46102233..46104443-chr17:46148232..46151120,2	K562	blood:
8	chr17:46102704..46105485-chr17:46150295..46153343,3	MCF-7	breast:
9	chr17:46139248..46141644-chr17:46149941..46152183,2	K562	blood:
10	chr17:46143868..46147268-chr17:46149730..46152129,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000082641	Chromatin interaction
ENSG00000207947	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000108468	Chromatin interaction
ENSG00000005243	Chromatin interaction

Extended variants
information (count: 107 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs1010228	0.83[ASN][1000 genomes]
rs1010230	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11079806	0.94[ASN][1000 genomes]
rs11079808	0.91[ASN][1000 genomes]
rs11079809	0.83[ASN][1000 genomes]
rs11649919	1.00[ASN][1000 genomes]
rs11651097	1.00[ASN][1000 genomes]
rs11655407	1.00[ASN][1000 genomes]
rs12450620	0.98[ASN][1000 genomes]
rs12600980	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12601350	0.93[EUR][1000 genomes]
rs12602131	0.93[EUR][1000 genomes]
rs12602670	0.93[EUR][1000 genomes]
rs12936731	0.98[ASN][1000 genomes]
rs12939514	0.82[ASN][1000 genomes]
rs12941295	0.91[ASN][1000 genomes]
rs12943543	0.91[ASN][1000 genomes]
rs12946143	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12949879	0.93[ASN][1000 genomes]
rs12950213	0.87[ASN][1000 genomes]
rs12950402	0.91[ASN][1000 genomes]
rs12952163	1.00[ASN][1000 genomes]
rs1468270	0.90[ASN][1000 genomes]
rs1473117	0.83[EUR][1000 genomes]
rs16951519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1860866	0.83[ASN][1000 genomes]
rs2023885	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2051821	1.00[ASN][1000 genomes]
rs208005	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs208008	0.86[AFR][1000 genomes]
rs208009	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs208019	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2109983	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2109984	0.91[ASN][1000 genomes]
rs2229369	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2240119	0.93[EUR][1000 genomes]
rs2240120	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2240121	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2285863	0.93[ASN][1000 genomes]
rs2325783	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2325784	0.81[EUR][1000 genomes]
rs2325804	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs35361214	1.00[ASN][1000 genomes]
rs35688835	0.91[ASN][1000 genomes]
rs3744346	0.83[ASN][1000 genomes]
rs3744347	0.87[ASN][1000 genomes]
rs3785737	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3815472	0.83[EUR][1000 genomes]
rs4794441	0.91[ASN][1000 genomes]
rs4794448	0.91[ASN][1000 genomes]
rs4794449	0.91[ASN][1000 genomes]
rs4794450	0.86[ASN][1000 genomes]
rs4794451	0.91[ASN][1000 genomes]
rs4794453	0.91[ASN][1000 genomes]
rs55920502	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58203448	1.00[ASN][1000 genomes]
rs58554000	0.95[EUR][1000 genomes]
rs58595405	1.00[ASN][1000 genomes]
rs58624511	0.98[ASN][1000 genomes]
rs62064953	0.90[ASN][1000 genomes]
rs6504024	1.00[ASN][1000 genomes]
rs6504025	1.00[ASN][1000 genomes]
rs6504031	0.91[ASN][1000 genomes]
rs6504032	0.89[ASN][1000 genomes]
rs6847	1.00[ASN][1000 genomes]
rs71356520	0.81[ASN][1000 genomes]
rs71356521	0.85[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs71369829	0.98[ASN][1000 genomes]
rs7209585	0.90[ASN][1000 genomes]
rs7209730	0.83[ASN][1000 genomes]
rs7212202	0.98[ASN][1000 genomes]
rs7213339	0.82[ASN][1000 genomes]
rs7217496	1.00[ASN][1000 genomes]
rs7220520	0.95[ASN][1000 genomes]
rs7221441	0.95[ASN][1000 genomes]
rs7222136	0.83[ASN][1000 genomes]
rs7224014	1.00[ASN][1000 genomes]
rs7224461	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72823528	0.93[EUR][1000 genomes]
rs72823532	0.93[EUR][1000 genomes]
rs72823533	0.93[EUR][1000 genomes]
rs741058	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs757353	0.93[EUR][1000 genomes]
rs8065670	0.91[ASN][1000 genomes]
rs8065993	0.91[ASN][1000 genomes]
rs8066049	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8066391	0.89[ASN][1000 genomes]
rs8071199	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8075500	0.89[ASN][1000 genomes]
rs8076380	0.91[ASN][1000 genomes]
rs8077860	0.91[ASN][1000 genomes]
rs8078125	1.00[ASN][1000 genomes]
rs8079616	0.83[EUR][1000 genomes]
rs8080662	0.91[ASN][1000 genomes]
rs875065	1.00[ASN][1000 genomes]
rs875066	1.00[ASN][1000 genomes]
rs9747001	0.99[ASN][1000 genomes]
rs978263	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9807087	0.83[ASN][1000 genomes]
rs9890691	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9899275	0.98[ASN][1000 genomes]
rs9899461	0.98[ASN][1000 genomes]
rs9910516	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
3	esv1804681	chr17:46144628-46168544	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv908576	chr17:46147807-46260366	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4995899	CBX1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46130400-46154600	Strong transcription	Primary T cells from cord blood	blood
2	chr17:46131200-46154200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:46131400-46151000	Strong transcription	Thymus	Thymus
4	chr17:46131400-46154400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr17:46131400-46154400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr17:46132600-46155200	Strong transcription	Fetal Thymus	thymus
7	chr17:46133000-46154600	Strong transcription	Fetal Brain Female	brain
8	chr17:46133000-46155200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr17:46133200-46157200	Strong transcription	Fetal Stomach	stomach
10	chr17:46133400-46151000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr17:46133400-46154400	Strong transcription	Brain Germinal Matrix	brain
12	chr17:46133400-46154400	Strong transcription	Rectal Mucosa Donor 29	rectum
13	chr17:46133400-46154600	Strong transcription	Primary T helper cells PMA-I stimulated	--
14	chr17:46133400-46155200	Strong transcription	Dnd41	blood
15	chr17:46133600-46151400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr17:46133600-46154400	Strong transcription	Primary neutrophils fromperipheralblood	blood
17	chr17:46133600-46154400	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr17:46133600-46154600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr17:46134000-46154200	Strong transcription	Stomach Smooth Muscle	stomach
20	chr17:46134400-46154400	Strong transcription	Primary B cells from peripheral blood	blood
21	chr17:46135400-46155400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr17:46137400-46155200	Strong transcription	Fetal Muscle Trunk	muscle
23	chr17:46137800-46151600	Weak transcription	Stomach Mucosa	stomach
24	chr17:46137800-46154600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr17:46138000-46154400	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr17:46139200-46162600	Weak transcription	Small Intestine	intestine
27	chr17:46139800-46162600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr17:46139800-46163600	Weak transcription	Esophagus	oesophagus
29	chr17:46140000-46153800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr17:46140000-46162400	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr17:46140200-46156400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr17:46140800-46163200	Weak transcription	Colonic Mucosa	Colon
33	chr17:46142200-46154400	Strong transcription	Fetal Muscle Leg	muscle
34	chr17:46142400-46153600	Weak transcription	Gastric	stomach
35	chr17:46142600-46153400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr17:46142600-46162600	Weak transcription	Fetal Heart	heart
37	chr17:46143600-46151400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr17:46143600-46157400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr17:46143800-46153400	Weak transcription	Spleen	Spleen
40	chr17:46143800-46154400	Strong transcription	H1 Cell Line	embryonic stem cell
41	chr17:46143800-46163200	Weak transcription	Aorta	Aorta
42	chr17:46144200-46154400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr17:46144200-46157000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr17:46144400-46152000	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr17:46144400-46153600	Weak transcription	Ovary	ovary
46	chr17:46144400-46154400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr17:46144400-46154400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr17:46144400-46154600	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr17:46144400-46163000	Weak transcription	Psoas Muscle	Psoas
50	chr17:46144600-46151400	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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